title: Hi-C-mid-G1-rep2

description: Hi-C

data_processing:
Paired-end reads were aligned independently to mm9 mouse genome using bowtie2 (global parameters: --very-sensitive –L 30 –score-min L,-0.6,-0.2 –end-to-end --reorder;  local parameters: --very-sensitive –L 20 –score-min L,-0.6,-0.2 –end-to-end --reorder) through the HiC-Pro software. Unmapped reads, non-uniquely mapped reads, and PCR duplicates were filtered, and uniquely aligned reads were paired. Reads from across sequencing runs and replicates (Rep1, Rep2) were pooled, then used to construct raw contact matrices at 10 kb resolution.
HiC preprocessing data processing step: Paired-end reads were aligned independently to mm9 mouse genome using bowtie2 (global parameters: --very-sensitive –L 30 –score-min L,-0.6,-0.2 –end-to-end --reorder;  local parameters: --very-sensitive –L 20 –score-min L,-0.6,-0.2 –end-to-end --reorder) through the HiC-Pro software. Unmapped reads, non-uniquely mapped reads, and PCR duplicates were filtered, and uniquely aligned reads were paired. Reads from across sequencing runs and replicates (Rep1, Rep2) were pooled, then used to construct raw contact matrices at 10 kb resolution.
HiC domain calling data processing step: Raw contact matrices were balanced using the Knight-Ruiz matrix balancing algorithm and quantile normalized across all five timepoints (prometa, anatelo, earlyG1, midG1, and lateG1). Domains were then called using 3DNetMod with published parameters. Consistent parameter adjustments were implemented across all time points: 0 minutes, 25 minutes, 60 minutes, 120 minutes, and 240 minutes on quantile normalized merged data at 10 kb resolution. Genome-wide counts data were logged and chunked into 7.5 MB regions with 5 MB overlap. A permissive filter threshold maximum 500 kb consecutive zeros in diagonal and minimum 2/3 nonzero counts coverage in central diagonal of chunked region was used for region acceptance (all regions except empty regions at beginning and end of chromosome or centromere/telomeres). For gamma selection, a restrictive minimum “plateau” size of 30 was used to induce more stable persistent calls (i.e. at least 30 consecutive gamma values, every 0.01 gamma step, with same mean number of called domains per 20 attempts, at each successive gamma). Optimal mean gamma value of each plateau was then selected for hierarchical domain detection. An adjusted rand index (arand) consensus call was then determined from a partition size of 20 attempts for each selected plateau gamma value. Additionally, a minimum domain size threshold of 150 kb was selected. For post processing, a restrictive maximum partition block variance threshold for called domains of 12 bins around each domain boundary across all sizes was chosen. Final initial domain calls per time point underwent a merging step, wherein calls within a single bin at both boundaries were subsumed into a single call with a merged start boundary declared at furthest upstream and stop boundary declared at furthest downstream of merged calls.
HiC stripe calling data processing step: Raw contact matrices were filtered to remove regions of low mappability and extreme outliers, then balanced using the Knight-Ruiz matrix balancing algorithm. We then applied a modified version of the stripe calling approach from (Vian et al. 2018). Briefly, we computed local horizontal and vertical signals from the raw contact matrix by finding the median of 10 pixels orthogonal to each query pixel. For the vertical signals, the median was calculated with respect to 5 pixels directly above and below, and for the horizontal signals, the median was calculated with respect to 5 pixels directly left and right. We then evaluated the local neighborhood around each pixel by convolving over the balanced contact matrix using top, bottom, left, and right footprints. Then, we computed the vertical and horizontal signals in the balanced matrix using the same logic as used for the raw matrix to generate bias factors that allow deconvolution of the directional footprints for statistical testing. Finally, to compute the expected background signal, we multiplied the left and right values by the bias factor and selected the maximum value. To compute the expected background signal, we multiplied the top and bottom values by their own bias factor instead. We assumed that the horizontal and vertical signals followed independent Poisson distributions parameterized by their background expected signals, testing whether the observed horizontal and vertical signals were higher than their expected signals. After obtaining Poisson p-values, we filtered and clustered significant pixels into stripes. First, we filtered out pixels with p-values greater than 0.15 and fold-changes less than 1.5. We also discarded pixels that had observed values less than 2 in the balanced contact matrix. After filtering, we clustered directly adjacent pixels in the vertical and horizontal directions separately. Horizontal and vertical clusters containing less than 3 pixels were thrown out. Then, we carried out a second clustering step where we merged surviving clusters with nearby clusters in the same direction. The maximum allowed distance between two clusters was 20 pixels. Once nearby clusters were merged, only those with 12 pixels or more were kept. Then, directly adjacent clusters in the orthogonal direction were merged together. The maximum cluster width was capped at 5 pixels.
HiC loop calling data processing step: Raw contact matrices were filtered to remove regions of low mappability and extreme outliers, then balanced using the Knight-Ruiz matrix balancing algorithm. Expected models were constructed using the maximum of the donut and lower left filters for pixels with interaction distances between 100 kb and 10 Mb, and our new “upper triangular” donut filter for pixels with interaction distances within 100 kb. P-values were computed for each pixel under a Poisson model, comparing the raw count for each pixel with the deconvoluted (using the Knight-Ruiz bias vectors) expected value for that pixel. Q-values were computed for each pixel using a combination of lambda-chunking and BH-FDR. Clusters of at least three neighboring significant pixels were identified and refined by applying progressively more stringent q-value thresholds, starting from the set of pixels significant at a FDR of 1%. Pixels with low observed counts or fold change between observed and expected values were removed from consideration prior to clustering. Refined clusters including pixels with interaction distances of 20 kb or less were removed.
HiC processed data files format and content: The processed data files <timepoint>_<stage>_intrachromosomal_contact_matrices.tar.gz are gzipped tarballs containing the 10kb resolution contact matrices for the pooled HiC libraries for <timepoint> (prometa, anatelo, earlyG1, midG1, or lateG1) at the <stage> (raw, kr, or qnorm) step of the data processing. The tarballs contain files <timepoint>_<stage>_<chromosome>.matrix, which contain the intrachromosomal contact matrix for each chromosome. Each line of a .matrix file represents an interaction between two bins on that chromosome. The .matrix files are formatted as tab delimited files with three columns, which represent the start coordinate of the upstream bin, the start coordinate of the downstream bin, and the value of the interaction, respectively. The end coordinates of the bins can be determined by adding the matrix resolution (10000 or 40000) to the start coordinate. For example, the line "10000<tab>40000<tab>10" in a 10kb resolution matrix file for chr1 should be interpreted to mean that the bin chr1:10000-20000 interacts with the bin chr1:40000-50000 with quantitative value 10. Bin-bin pairs with zero reads, or values that have been filtered out during processing are not listed in the matrix files. Therefore not every possible bin-bin pair has a corresponding line in the matrix file. Such bin-bin pairs can be assumed to

extract_protocol:
5million pro-meta or ana/telo cells and 10million interphase cells were collected from cell sorting per experiment. Cells were pelleted, re-suspended in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) and incubated on ice for 10min. Cell nuclei was pelleted at 4℃ and washed with 800ul 1.2xDpnII buffer. Nuclei was pelleted at 4℃ and re-suspended in 500ul 1.2xDpnII buffer. 15.5ul SDS (10%) was added into the system to reach a final concentration of 0.3%. Samples were then incubated at 37℃ on a thermomixer for 1h with shaking at 950rpm. 50ul Triton X-100 (20%) was added to the system to reach a final concentration of 1.8%. Samples were further incubated at 37℃ on a thermomixer for 1h at 950rpm. 300U of DpnII restrictive enzyme (NEB, R0543M) was then added into the system and samples were incubated at 37℃for overnight with shaking at 950rpm. Another 300U of DpnII was added into the system and samples were further incubated at 37℃ for 2-4h with shaking at 950rpm. Samples were then incubated at 65℃ for 20min with shaking at 950rpm to inactivate DpnII. Nuclei was pelleted, cooled down to room temperature, re-suspended in 300ul 1xNEB buffer2, containing 50uM biotin-14-dATP (Thermal Fisher Scientific, 19524016), dGTP, dCTP, dTTP (Promega, U121B, U122B, U123B) and 40U DNA Polymerase I, Large (Klenow) fragment (NEB, M0210) and incubated at 37℃ for 1.5h with shaking at 950rpm. The system was then added with 120ul 10xT4 DNA ligase buffer, 12ul 100xBSA, 758ul nuclease free water and 10ul (4000U) T4 DNA ligase (NEB, M0202M). Ligation was carried out at 16℃ for 4h and room temperature for additional 2h. 20ul of 20mg/ml protease K (3115879 BMB) and 120ul of 10%SDS were added into the system and samples were de-crosslinked at 65℃ for overnight. An additional 10ul of protease K was added and samples were further de-crosslinked at 55℃ for 2h. DNase-free RNase was added into the system and samples were incubated at 37℃ for 30min. Ligated DNA was extracted with phenol chloroform extraction and re-constituted in 180ul nuclease free water. DNA concentration was quantified with a Qubit 4 Fluorometer (Thermal Fisher Scientific, Q33226). Ligated DNA was sonicated to 200-300bp (Epishear, Active Motif, 100% amplitude, 30s ON and 30s OFF, 25-30min) and cleaned up with AMPure XP beads (Beckman Coulter). Each sample of biotinylated DNA was pulled down with 100ul Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, 65002) by incubating at room temperature for 15min. The amount of bound DNA was calculated by subtracting the amount of unbound DNA from the amount of total DNA. DNA bound streptavidin beads were washed once with 1xbead wash buffer (5mM Tris-HCl (pH 7.5), 0.5mM EDTA and 1M NaCl) and once with T4 DNA ligase buffer. Streptavidin beads were re-suspended with 84ml water.
Library was prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040, M0543L, E7335S) according to manufacture instruction. On-bead end repair was performed by mixing 84ul biotinylated beads with 10ul NEBNext End Repair Reaction Buffer (10x), 5ul NEBNext End Repair Enzyme Mix and 5U DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210). The mixture was incubated at room temperature for 30min. Beads with end repaired blunt DNA was washed once with 600ul 1xbead wash buffer and then 500ul 1xNEB buffer2. Beads was re-suspended in 42ul nuclease free water. Beads were then mixed with 5ul NEBNext dA-tailing reaction buffe (10x) and 3ul Klenow Fragment (3’→5’ exo-) for dA-tailing. The mixture was incubated at 37℃ for 30min. Beads were then washed once with 600ul 1xbead wash buffer and then 600ul 1xT4 DNA ligase buffer.  Beads were re-suspended in 20ul nuclease free water. Adaptor ligation was performed by mixing the beads with 10ul Quick Ligation reaction buffer (5x), 15ul NEBNext Adaptor (15uM) and 5ul Quick T4 ligase. The mixture was incubated at room temperature for 15min. 3ul of USER enzyme was then added into the mixture and incubated at 37℃ for 15min. Beads were washed twice with 600ul 1xbead wash buffer and re-suspended in 50ul nuclease free water containing 0.1% SDS. Beads were incubated at 98℃ for 10min to release DNA and DNA was cleaned up with AMPure XP beads. Purified adaptor ligated DNA was then index labeled with NEBNext multiplex oligos for 6 cycles on a thermal cycler. PCR products were purified using AMPure XP beads. Sequencing was performed on an Illumina NextSeq 500 platform using Illumina sequencing reagents according to manufacturer’s instructions.


title: Hi-C-late-G1-rep1

status: Public on Nov 27 2019

type: SRA

city: Philadelphia

first: Gerd

middle: A

last: Blobel

state: PA

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

country: USA

institute: University of Pennsylvania	Children's Hospital of Philadelphia

description: Hi-C

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

treatment_protocol: Cells were synchronized to pro-metaphase with 200ng/ml nocodazole for 7-8.5h. For post-mitotic enrichment, cells were released from nocodazole for 0, 25min, 60min, 120min and 240min for pro-meta, ana/telo, early-G1, mid-G1 and late-G1 respectively.

tag: cell type

value: erythroid

tag: strain


title: Hi-C-early-G1-rep1

description: Hi-C


title: ChIP-seq-CTCF-late-G1-rep1

description: ChIP-seq

data_processing:
Sequencing reads were mapped to the reference mouse genome mm9 using bowtie (0.12.7, "-m 2 --tryhard"). Reads were filtered to remove non-uniquely mapped reads and PCR duplicates using SAMtools (v1.7, "samtools rmdup -s") and converted to bed format using BEDtools (v2.27.1, "bedtools bamtobed"). Peaks were identified using the MACS2 (v2.1.0, "macs2 callpeak") with punctate calling for both CTCF and Rad21 (p-values 1e-8 and 1e-4 respectively), using each IP's cell cycle stage matched input as the control.
Genome_build: mm9

extract_protocol:
For each IP, 7-10million crosslinked cells were re-suspended in 1ml Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) containing fresh protease inhibitors (Sigma P8340) and 1mM phenylmethylsulfonyl fluoride (PMSF) for 20min on ice. Nuclei was pelleted at 4℃ and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS) containing fresh protease inhibitors and PMSF and incubated for 20min on ice. Samples were added with 0.6ml IP Dilution Buffer (20mM Tris pH 8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing fresh protease inhibitor and PMSF and then subject to sonication for 45min (Epishear, Active Motif, 100% amplitude, 30s ON and 30s OFF, ~45min). After sonication, samples were spun at 21130g at 4℃ for 10min to pellet cell debris. Supernatant was transferred to a new tube and supplemented with 3.4ml IP Dilution Buffer containing fresh protease inhibitor, PMSF, protein A/G agarose beads (prepared by mixing protein A (Thermo Fisher Scientific 15918014) and protein G (Thermo Fisher Scientific 15920010) agarose beads at 1:1 ratio) and 50mg isotope matched IgG. Chromatin preclear was carried out for over 2h at 4℃. 200ml (4%) of precleared chromatin was taken out from subsequent IP steps and set as input. Pre-cleared chromatin was then added to protein A/C beads bound with antibodies and incubated overnight with rotation at 4℃. After IP, beads were washed once with IP Wash Buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with PE Buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing and pelleting steps were performed on ice or at 4℃. Beads were then moved to room temperature and eluted twice with 100ml freshly prepared Elution Buffer (100mM NaHCO3, 1%SDS) to reach a final concentration of 200ml. Eluted samples were supplemented with 12ml 5M NaCl, 2ml DNase-free RNaseA (10mg/ml, 10109169001 BMB) and incubated at 65℃ for overnight. Samples were then added with 3ml protease K (20mg/ml, 3115879 BMB) and further de-crosslinked at 65℃ for 2h. De-crosslinked DNA was added with 10ml 3M sodium acetate pH 5.2 and purified with QIAquick PCR Purification kit (QIAGEN 28106) according to manufacture instruction.
Library construction was performed using Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012) according to manufacturer’s specifications with the addition of size selection (left side at 0.9x, right side at 0.6x) using SPRIselect beads (Beckman Coulter, catalog no. B23318) prior to PCR amplification. Library size was determined (average 351 bp, range 333-372 bp) using the Agilent Bioanalyzer 2100, followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Libraries were then pooled and sequenced on the Illumina NextSeq 500 platform using Illumina sequencing reagents according to manufacturer’s instructions


title: ChIP-seq-CTCF-mid-G1-rep2

description: ChIP-seq


title: Hi-C-ana.telo-rep2

description: Hi-C


title: Hi-C-late-G1-rep2

description: Hi-C


title: Capture-C-early-G1-rep3

description: Capture-C

data_processing:
Raw read quality were assessed with Trim Galore (a wrapper for FastQC and Cutadapt). Trimmed reads were merged or interleaved using FLASH 1.2.8. Concatenated reads were then in silico digested with DpnII, aligned to mm9 and analyzed using CCAnalyzer3. Interactions were normalized to total interactions to generate bedgraph files for each bait/condition. Bedgraph files from each individual replicate was merged.
Genome_build: mm9

extract_protocol:
Capture-C experiments were performed as previously described (Hughes et al. Nat. Genet. 2014, Huang et al. Genes Dev. 2017). 3C library preparation was similar to that of in-situ HiC experiments without biotin nucleotide labeling. Briefly, cells were fixed with 1% PFA and sorted at designated cell cycle stages. DNA was directly ligated after DpnII digestion, extracted with pheno-chloroform and fragmented.
Ligated DNA was purified, fragmented and converted into 3C library using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040, M0543L, E7335S). After indexation with NEBNext multiplex oligos, DNA was cleaned up with AMPure XP beads and further amplified with Illumina P5 and P7 primers for 6 cycles. To perform oligo pull-down, 3C libraries were completely dried on a thermal cycler at 60℃. Dried DNA was re-constituted with 13ul hybridization mixture (2.5ul nuclease free water, 7.5ul 2xhybridization buffer, 3ul hybridization component A, Nimblegen SeqCap Hybridization and Wash kit) for 10min at room temperature. DNA was denatured at 95℃ for 10min and then added with 2ul 3pmole biotin-labeled capture probe pool to make a 15ul hybridization system. Hybridization was immediately carried out at 47℃ for more than 24h on a thermal cycler. Hybridized DNA was pulled down with Dynabeads MyOne Streptavidin C1 beads (40ul per capture) and washed with Nimblegen SeqCap Hybridization and Wash kit according to manufacture instruction. Captured DNA was then eluted into 25ul 0.125N NaOH, followed by HCl neutralization. Captured DNA was then purified with AMPure XP beads. Purified DNA was then amplified with Illumina P5 and P7 primer for 12 cycles and PCR products were cleaned up with AMPure XP beads. PCR products were dried on a thermal cycler at 60℃ to initiate a similar second round of capture for further enrichment of targeted DNA. DNA was eluted into 25ul nuclease-free water and subject to sequencing with Illumina NextSeq 500 platform using Illumina sequencing reagents according to manufacturer’s instructions.


title: Capture-C-mid-G1-rep2

description: Capture-C


title: Capture-C-ana.telo-rep3

description: Capture-C


title: Hi-C-ana.telo-rep1

description: Hi-C


title: Hi-C-prometa-rep1

description: Hi-C


title: Capture-C-prometa-rep3

description: Capture-C


title: Capture-C-prometa-rep2

description: Capture-C


title: Capture-C-early-G1-rep2

description: Capture-C


title: Capture-C-mid-G1-rep3

description: Capture-C


title: Capture-C-ana.telo-rep2

description: Capture-C


title: Capture-C-mid-G1-rep1

description: Capture-C


title: Capture-C-prometa-rep1

description: Capture-C


title: Control [ATAC-seq]

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

description: processed data file: ATAC_intervals.csv

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina (NextSeq 500) sequencing were mapped to the reference genome UCSC hg38 using the BWA algorithm with default settings.
Genomic regions with high levels of transposition/tagging events were determined using the MACS2 peak calling algorithm.
The genome was divided into 32 bp bins and the number of fragments in each bin was determined.
To compare peak metrics between 2 samples, overlapping Intervals were grouped into “Merged Regions”, which were defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals). In locations where only one sample has an Interval, this Interval defines the Merged Region.
The top differential regions were identified using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC_intervals.csv: Comma-separated text file

organism: Homo sapiens

source_name: H1299 cells

growth_protocol: The lung cancer cell line H1299 (ATCC, CRL-5803) was obtained from the American Type Culture Collection (ATCC). The cells were cultured in RPMI 1640 medium (Lonza, Allendale, NJ) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed at the Active Motif (Carlsbad, CA).

treatment_protocol: The cells were treated with or without 5mM metformin (D150959, Sigma-Aldrich, St. Louis, MO).

value: Non-small cell lung cancer cell line

tag: passages

tag: treatment


title: Capture-C-ana.telo-rep1

description: Capture-C


title: Hi-C-mid-G1-rep1

description: Hi-C


title: Metformin [ATAC-seq]

description: processed data file: ATAC_intervals.csv

value: Metformin


title: Capture-C-early-G1-rep1

description: Capture-C


title: RNAExp31

city: Pleasanton

first: Maeve

last: Ohuallachain

state: CALIFORNIA

address: 4300 Hacienda Drive

institute: ROCHE SEQUENCING SOLUTIONS INC

library_source: transcriptomic

data_processing:
Library strategy: Single cell barcoding by split-pool synthesis via ligation
FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.

molecule: total RNA

source_name: Jurkat cell line and Nalm6 cell line

growth_protocol: Jurkat cells and Nalm-6 cells were obtained from America Type Tissue Collection (ATCC). Cells at a density of ~1×106/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells were pelleted and permeabilized with ice-cold methanol for at least 10 min on ice. Once in methanol cells can be stored at −80 °C for several weeks without loss of antibody signal or RNA degradation.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers

tag: cell line

value: Jurkat cell line and Nalm6 cell line

tag: molecule type

value: various targeted RNA transcripts


title: RNAExp26


title: RNAExp29


title: Hi-C-prometa-rep2

description: Hi-C


title: Exp77

source_name: PBMC primary cells from donor

growth_protocol: Cells at a density of ~1×10^6/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells to be analyzed for only protein expression were stored in 1X PBS with 10% DMSO at -80°C until antibody staining.

value: PBMC primary cells from donor

value: various proteins


title: Hi-C-early-G1-rep2

description: Hi-C


title: RNAExp30_S3

organism:
Homo sapiens
Mus musculus

source_name: Nalm6 cell line and BW5147 cell line

growth_protocol: Nalm-6 cells and BW5147 cells were obtained from America Type Tissue Collection (ATCC). Cells at a density of ~1×10^6/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells were pelleted and permeabilized with ice-cold methanol for at least 10 min on ice. Once in methanol cells can be stored at −80 °C for several weeks without loss of antibody signal or RNA degradation.

value: Nalm6 cell line and BW5147 cell line


title: Patient3-Vemurafenib3

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

data_processing:
Pair-end read received adapters removed
Reads are aligned to hg19 genome using tophat (v2.0.13)/Bowtie version:2.2.3.0
Gene expression is assessed with HTSeq-0.6.1 as the raw read count at gene level
Normalization and differential expression are analyzed with DESeq2 (v1.24.0)
Genome_build: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
Supplementary_files_format_and_content: Raw read count generated with HTSeq-0.6.1
Supplementary_files_format_and_content: Normalized read count from counts_raw.csv with DESeq2

extract_protocol: WM164 cells were plated in a 6-well plate at 200,000 cells/well and allowed to attach overnight in normal culture media. Next day, the media was replaced to serum-free RPMI and cells were incubated overnight. Cells were treated with 3μM vemurafenib or vehicle control in 5% FBS/RPMI, or a 1:1 mixture of serum-free media:CSF from patient 1, patient 2 or patient 3 for 8 hours. RNA was extracted using Qiagen’s RNeasy Kit, with on-column DNase digestion (Hilden, Germany). RNA samples were reviewed for quality on the Agilent TapeStation followed by quantitation using the Qubit fluorometric assay.  RNAseq libraries were processed using the Ovation Human FFPE RNA-Seq Multiplex System (NuGEN Technologies, San Carlos, CA). Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.  BioAnalyzer library size assessment and the Kapa Library Quantification Kit were used for library quantification.  The libraries were sequenced on the Illumina NextSeq 500 v2 sequencer with two 75-base paired-end runs in order to generate 25-35 million read pairs per sample.

tag: agent

value: 3uM PLX4032 in context of Patient 3 CSF


title: Patient3-Vemurafenib1


title: Patient3-Vemurafenib2


title: Patient3-control3

value: vehicle control in context of Patient 3 CSF


title: Patient3-control1


title: RNAExp30_S2


title: Patient3-control2


title: Patient2-control3

value: vehicle control in context of Patient 2 CSF


title: Patient1-Vemurafenib3

value: 3uM PLX4032 in context of Patient 1 CSF


title: Patient2-Vemurafenib3

value: 3uM PLX4032 in context of Patient 2 CSF


title: Patient1-control2

value: vehicle control in context of Patient 1 CSF


title: Patient2-control2


title: iRKO_VEH_DEN_ZE-25-MR91

city: Cambridge

first: Jun

last: Shi

state: MA

address: 181 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

data_processing:
The 76bp paired-end reads were mapped to mouse genome mm10 using STAR 2.4.5a with default parameters.
A genome-wide transcription signal map was derived by counting reads coverage in 10 bp step after normalizing to 1 million total reads. Stranded information was used to separate counts from sense and antisense strand.
For gene annotation, we first clustered the Refseq transcripts based on the sharing of splicing sites to get a master set of gene loci representing all alternative isoforms.
Signal from sense-strand were averaged across the exonic regions for each gene locus and normalized to TPM (Transcripts Per Million).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: Gastrocnemius muscle

extract_protocol:
Snap frozen gastrocnemius muscles were ground in liquid nitrogen by mortar and pestle and total RNA was extracted from ~20 mg of tissue powder using miRNeasy Micro Kit (Qiagen, 217084). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies, USA) and the integrity validated by the OD260/OD280 absorption ratio (>1.8) and by RIN score (>8) using Agilent 2100 Bioanalyzer, RNA 6000 Nano LabChip kit and Agilent 2100 Expert Software (Agilent Technologies, Inc., Santa Clara, CA, USA).
Stranded polyA+ RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HDAC4flox+/- mice carrying a floxed HDAC4 allel with exon 5 flanked by two loxP sites were mated to Taconic ROSA26-Cre-ERT2 transgenic line (Taconic Biosciences, Rensselaer, New York), which express a conditional Cre-ERT2 recombinase from the ROSA26 locus. Exon 5 deletion would result in a frameshift mutation in the HDAC4 allele causing premature termination of protein translation. Ubiquitous induction of Cre activity could be observed in all tissues after intraperitoneal injection of tamoxifen. To induce Cre expression, tamoxifen (dissolved in corn oil at 10 mg/ml) was administered intraperitoneally to four-month-old mice at a dose of 40 mg/kg for seven consecutive days. Four weeks later, a tail biopsy was taken and RNA isolated to evaluate the degree of HDAC4 knockout by quantitative real-time PCR. Six-weeks after tamoxifen injection, animals were subjected to unilateral sciatic neurectomy (denervation). On the day of sergery, animals started to receive treatment with vehicle (0.5% Methylcellulose, 0.5%Tween 80 in water, pH 6.5) or NVS-HD1 by oral gavage twice daily (10/14 hour intervals). Body weight and food intake were monitored twice weekly before and throughout the study. At the end of the study, mice were sacrificed and muscles from both hind legs and visceral organs were carefully dissected out, weighed and snap frozen in liquid nitrogen.

tag: genotype

value: HDAC4 inducible whole-body knockout

value: vehicle

tag: denervation surgery

value: denervated leg


title: RNAExp30_S1


title: Patient2-Vemurafenib1


title: Patient1-control3


title: iRKO_VEH_DEN_VE-25-MV91


title: Patient1-control1


title: 5PT-FBSVemurafenib3

value: 3uM PLX4032 in 5percent FBS/RPMI


title: Patient1-Vemurafenib2


title: iRKO_VEH_DEN_NE-26-MD91


title: iRKO_VEH_DEN_RE-25-MZ91


title: 5PT-FBSVemurafenib2


title: 5PT-FBSVemurafenib1


title: iRKO_VEH_DEN_JE-26-MH91


title: iRKO_VEH_DEN_JD-27-XL93


title: 5PT-FBScontrol2

value: vehicle control in 5percent FBS/RPMI


title: iRKO_VEH_DEN_ND-27-XH93


title: 5PT-FBScontrol3


title: iRKO_VEH_DEN_DE-25-MO91


title: iRKO_VEH_DEN_HE-25-MK91


title: WT_NVS-HD1_DEN_XD-27-IC95

value: wild-type


title: 5PT-FBScontrol1


title: Patient2-Vemurafenib2


title: Patient1-Vemurafenib1


title: Patient2-control1


title: THP1_DSMZ1

city: Liege

first: Gregory

last: Ehx

state: Liege

address: Avenue de l'Hopital, 1

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Acute monocytic leukemia cell line (THP-1) obtained from DSMZ, collected in log phase of expansion.

data_processing:
Basecalls performed using Illumina RTA 2.4.11
Samples demultiplexed using bcl2fastq 2.20
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference transcriptome using kallisto 0.43.0.
TPM values were computed by kallisto using a transcriptome index built on human genome GRCh38 along with Ensembl 88 annotations.  An estimated fragment length of 300bp and standard deviation of 50bp was used as parameters for the analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression files are tab delimited with columns 1) Ensembl transcript identifier, 2) transcript length , 3) effective transcript length, 4) estimated counts, and 5) transcript per million reads sequenced (TPM).

molecule: polyA RNA

source_name: THP-1 cell line

growth_protocol: THP-1 cells were seeded in RPMI+20%FBS at a concentration of 0.2 millions / ml, expanded for 48h (37°C, 5% CO2), split 1:2 and expanded for 24h before collection (final density = 0.5 millions / ml). ATCC and DSMZ cells were cultured simultaneously in identical conditions. Replicates of each expansion (ATCC or DSMZ) were performed independently.

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA HyperPrep Stranded PolyA

treatment_protocol: No treatment performed

tag: manufacturer

value: DSMZ

tag: replicate


title: WT_NVS-HD1_DEN_LD-27-IO95


title: THP1_ATCC1

description: Acute monocytic leukemia cell line (THP-1) obtained from ATCC, collected in log phase of expansion.

value: ATCC


title: WT_NVS-HD1_DEN_HD-27-IS95


title: In Vivo 2 [M543]

first: Devon

last: Svoboda

email: svobodadevon@gmail.com, barc@wi.mit.edu

address: 455 Main St

institute: Whitehead Institute

description: 657 iPSCs were reprogrammed from fibroblasts (Couriel) and targetted to express GFP constitutively.

data_processing:
Fastq files were obtained with using "cellranger mkfastq" (Cell Ranger v3 from 10x Genomics).
Demultiplexing, mapping and gene counting were performed with "cellranger count", Cell Ranger 3.0.2 from 10x Genomics.
For samples IV1 and IV2, mapping was done against the human release hg18 plus the sequence coding for the green fluorences protein EGFP. For the other 4 samples Mapping was done  against a combined genome containing hg18, mm10 amd the sequence coding for the green fluorences protein EGFP.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

source_name: GFP+ cells from chimeric mouse brain

growth_protocol: Microglial Precursors from 657-GFP iPS cell line using protocol published in Douvaras et al. 2017.  Further differentiated in vitro using a new media containing TGFB1, CSF1 and IL34 published in Svoboda et al., 2019, PNAS.

extract_protocol:
In vivo samples were extracted by homogenizing the mouse brain on ice and FACS sorting out GFP+ cells for library construction.  In vitro samples were extracted by detaching cells from the cell culture dish using EDTA, running cells through the brain homogenization protocol to control for effects of protocol, and FACS sorting GFP+ cells. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps. Cell count was determined using Countess II.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns PN-1000075, according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

tag: source detailed

value: From NSG-Tg(Hu-SCF, GM-CSF, IL-3, CSF1) chimeric mouse

value: 657-GFP iPS cell line


title: In Vivo 1 [M544]


title: ZNF544_iso1

city: Huntsville

first: Eric

middle: M

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

institute: HudsonAlpha Institute

data_processing:
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates and 2 controls
ChIP-seq fastqs and ChIP-seq controls were aligned to hg19 genome assembly using BWA-0.7.12(Burrows Wheeler Aligner)
Post-alignment filtering was performed using samtools with MAPQ_THRESH=30 & picard-tools-1.88 to remove the duplicates
Peak enrichment was computed using phantompeakqualtools, implementing SPP peak calling algorithm, to generate narrowpeaks
IDR was run on replicates peak file and pooled peaks, using idr-2.0.2 tool, to generate peaks passing IDR cutoff 0.02 (soft-idr-threshold) followed by filtering of ENCODE blacklisted regions
Genome_build: hg19 male
Supplementary_files_format_and_content: NarrowPeak files are in BED6+4 format with 10 tab-delimited columns [chrom ,chromStart ,chromEnd ,name ,score ,strand ,signalValue ,pValue(-log10) ,qValue(-log10) , peak]; -1 used if no pValue, qValue assigned.

source_name: HepG2 cells

growth_protocol: HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)

extract_protocol:
Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol.
Illumina Single End for ChIP-seq

tag: chip antibody


title: WT_NVS-HD1_DEN_TD-27-IG95


title: THP1_DSMZ2


title: THP1_ATCC2


title: WT_NVS-HD1_DEN_PD-27-IK95


title: THP1_ATCC3


title: WT_NVS-HD1_DEN_HC-28-TW97


title: WT_NVS-HD1_DEN_DD-27-IW95


title: ZNF331


title: ZNF335


title: WT_VEH_DEN_VC-28-EN99


title: WT_NVS-HD1_DEN_BD-26-IZ95


title: THP1_DSMZ3


title: WT_VEH_DEN_JC-28-EZ99


title: ZSCAN29_iso1


title: WT_VEH_DEN_ZC-28-EJ99


title: ZNF281


title: WT_VEH_DEN_XC-29-EK99


title: ZHX3_iso1


title: ZC3H4


title: ZNF334_iso1


title: WT_VEH_DEN_RC-28-ER99


title: WT_NVS-HD1_DEN_FD-26-IV95


title: ZBTB21


title: ZCCHC11


title: WT_VEH_DEN_FC-29-ED99


title: WT_VEH_CON_VB-29-QR91

value: control contralateral leg


title: Myoblasts_MeDIP

city: Kunming

first: Chao

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

country: China

institute: Chinese Academy of Sciences

description: immunoprecipitated DNA with 5mC antibody

data_processing:
Basecalls performed using CASAVA
MeDIP reads were aligned to mouse genome (mm9) using bowtie2.
Samtools was used to convert SAM to BAM, and sort BAM files.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using bamCoverage (deeptools) with parameters --normalizeUsingRPKM

source_name: muscle

growth_protocol: Mouse C2C12 myoblasts were grown in 10% FBS to reach about 40-60% confluency, then were collected for following assays. Besides, when myoblasts were confluent, then we exchanged with fresh medium containing 2% horse serum. After keeping for 6 days, differentiated myotubes were collected for following assays.

extract_protocol:
Lysates were clarified from sonicated nuclei
In brief, DNA libraries were prepared with the NEB Next DNA Library Prep Master Mix Set for Illumina (E6040, NEB) following the manual provided by the manufacturer.First, fragmented DNA (200-500 bp) was end repaired and purification by AMPure XP Beads (A6380, Beckman). Then, purified DNA was added dA-tails and purified with AM-Pure XP Beads again. Subsequently, dA tailed DNA was ligated with adaptors. After purifi-cation, treated DNA was denatured at 99°C for 10 min, then placed the tube on ice immedi-ately. Next, DNA was incubated with the specific antibody against 5mC (BI-MECY-0100) at 4°C for 2 h and captured with protein A/G agarose beads at 4 °C for 2 h. After washing three times with IP buffer (140 mM NaCl, 0.05% Triton X-100, 3.9 mM NaH2PO4, 6.1 mM Na2HPO4) and digesting with proteinase K, the DNA fragments were extracted twice by phenol-chloroform and amplified by adaptor-mediated PCR. Subsequently, after purifica-tion, the DNA fragments were sequenced by the Illumina HiSeq 2000 sequencing platform.

tag: tissue

value: muscle

tag: parental cell line

tag: differentiated stage

value: 0 day

value: myoblast

tag: medip antibody

value: 5mC (Eurogentec, BI-MECY-0100)


title: Myotubes_Input

description: input

value: 6 days

tag: cell type

value: myotubes


title: UBP1

description:
Re-analysis of:
Raw file(s):
ENCFF308BBG_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR674ZLO


title: ZNF12


title: WT_VEH_DEN_BC-29-EH99


title: WT_VEH_CON_RB-29-QV91


title: WT_VEH_CON_ZB-29-QN91


title: Myotubes_MeDIP


title: Myoblasts_Input

description: input


title: THRA_iso1


title: WT_NVS-HD1_DEN_ZD-27-IZ95


title: WT_VEH_CON_JB-20-QD92


title: SP1


title: WT_VEH_CON_NB-29-QZ91


title: WT_VEH_CON_FB-20-QH92


title: PRDM10


title: RREB1_iso2


title: Input 4

description:
Re-analysis of:
GSM2423739 GSM2423740
Raw file(s):
ENCFF002ECQ ENCFF002ECU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR613TDP
Input for BACH1
Input for CUX1
Input for FOS
Input for HCFC1
Input for KAT2B
Input for NFE2L2
Input for SIN3B
Input for SUZ12
Input for TBL1XR1
Input for ZNF143
Input for ZNF384


title: PAXIP1_iso1


title: Input 40

description: Input for TCF12


title: WT_VEH_CON_DC-28-EG99


title: WT_VEH_CON_DB-29-QK91


title: ZNF384

description:
Re-analysis of:
GSM2423015 GSM2423014
Raw file(s):
ENCFF001YXE ENCFF001YXD
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR101FJU


title: ZNF143

description:
Re-analysis of:
GSM2423013 GSM2423012
Raw file(s):
ENCFF001YXF ENCFF001YXH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR101FJT


title: TCF7L2

description:
Re-analysis of:
GSM782122
Raw file(s):
ENCFF000XYV ENCFF000XYX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EVQ


title: TCF12


title: SIX4_iso1


title: NPAS2_iso2


title: TBL1XR1

description:
Re-analysis of:
Raw file(s):
ENCFF001YXI ENCFF001YXJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR101FJS


title: MTA1

description:
Raw file(s):
ENCFF188IKK_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR794UDP


title: Siah2-WT

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
scRNA-seq
PolyA RNA

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment were performed with 10x Genomics Cell Ranger software.
Indexed BAM files contain position-sorted reads aligned to the genome.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Siah2-WT.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: Siah2-KO.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: barcodes.tsv: raw barcodes
Supplementary_files_format_and_content: genes.tsv: raw genes
Supplementary_files_format_and_content: Siah2.counts.raw.csv: raw counts
Supplementary_files_format_and_content: Siah2.counts.normalized.csv: normalized counts
Supplementary_files_format_and_content: and gene-barcode matrices.

source_name: subcutaneously-engrafted tumor

extract_protocol:
Tumors from each group were minced prior to incubation with 0.3 Wünsch U/mL Liberase TM (Sigma) and 50 U/ml DNase I (Roche) in Hank’s Balanced Salt Solution (Life Technologies) for 30 min at 37°C with agitation. Tumors were homogenized by repeated pipetting and filtered through a 70-μm nylon filter. Single cell suspensions were washed with 1XPBS-4%FBS before incubation 20 min on ice at 5x10^7 cells/ml with 500 ng/ml Fc block (2.4G2, BD Pharmingen) to prevent non-specific antibody binding. Cells were then incubated 1 hour on ice with PE-eFluor610 conjugated CD45 monoclonal antibody (30-F11, eBioscience). DAPI-negative (live) CD45+ and CD45- cells were sorted using a SY3200 flow cytometer and sorted cells were resuspended in RPMI for counting. Live CD45+ and CD45- cells were mixed 5:1.
Libraries were prepared using a Single Cell 3’ Reagent Kit v2, a Chromium Single Cell 3’ Library & Gel Bead Kit v2 PN-120237, a Single Cell 3’ Chip Kit v2 PN-120236, and an i7 Multiplex Kit PN-120262 (10x Genomics), following the user guide from the Single Cell 3’ Reagent Kit v2 (Manual Part # CG00052 Rev A).

tag: strain/background

tag: genotype/variation

value: Wild type

value: YUMMER1.7 tumor

tag: duration

value: 11 days

tag: age of mice (weeks)

tag: Sex

value: Male


title: SUZ12

description:
Re-analysis of:
GSM2423950 GSM2423949
Raw file(s):
ENCFF002EEA ENCFF002EEF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR771GTF

tag: cell line


title: Siah2-KO

description:
scRNA-seq
PolyA RNA

value: Siah2 -/-


title: SIN3B

description:
Re-analysis of:
GSM2423502 GSM2423501
Raw file(s):
ENCFF002EDY ENCFF002EDW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR452YHM


title: HCFC1

description:
Re-analysis of:
GSM2423622 GSM2423623
Raw file(s):
ENCFF002EDS ENCFF002EDN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR529JYA


title: KDM2A


title: KDM3A

description:
Raw file(s):
ENCFF108YMB_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR387JKT


title: KAT2B

description:
Re-analysis of:
GSM2423752 GSM2423753
Raw file(s):
ENCFF002EDZ ENCFF002EED
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR620YNB


title: JARID2_iso1


title: HMGXB3


title: miR-7_purification2_0.4percent_rep1

first: Sean

middle: E.

last: McGeary

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

data_processing:
Each RBNS sequencing read was used if it satisfied the following criteria: 1) it passed the Illumina chastity filter, as indicated by the presence of the number 1 rather than 0 in the final position of the fastq header line, 2) it did not contain any “N” base calls, 3) it did not contain any positions with a Phred quality score (Q) of B or lower, 4) the sequenced 6-nt sample-multiplexing barcode associated with the read was identical to one of the barcodes used when generating the sequencing library, 5) it did not match either strand of the phi-X genome, 6) it did not nearly match (allowing up to two single-nucleotide-substitutions/insertion/deletions) the standards added to the samples during library workup, and 7) it contained either a TCG at positions 38–40 in the library of the experiment using the first AGO2–miR-1 preparation or a TGT at these positions for all other experiments.
Reads were first appended with 5 nt of adapter sequence on either end, and then queried for all site types or 12-nt k-mers relevant to the miRNA used in that AGO-RBNS experiment according to the methods.
Relative KD values are fit from the count data according to the methods.
Genome_build: NA
Supplementary_files_format_and_content: For each of the six miRNAs in this study, one purification was used to fit site counts, for which there is a tab delimited text file giving all identified combinations of the identified sites in each of the binding reactions of the AGO-RBNS experiment. There are four more tab-delimited text files associated with each of the six AGO2–miRNA complex purification used, providing ln(KD) values fit for four different sets of 12-nt k-mers, with each set containing a distinct 4-nt sequence of complementarity to the miRNA seed sequence.

organism: synthetic construct

source_name: in vitro transcribed RNA library

extract_protocol:
RNA extraction was prepared according to the methods.
RNA libraries were prepared for sequencing according to the methods.

treatment_protocol: AGO-RBNS was performed according to the methods.

tag: miRNA

tag: rbp

value: purified AGO2–miRNA complexes

tag: ago–mirna complex purification

tag: sampletype

tag: rep


title: miR-7_purification2_0percent_rep2


title: miR-7_purification2_0.4percent_rep2


title: FOXP1

description:
Raw file(s):
ENCFF452XLY_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR369YUK

tag: chip antibody


title: FOXK1


title: miR-7_purification2_0percent_rep1


title: miR-7_purification2_1.265percent_rep2


title: KAT7

description:
Raw file(s):
ENCFF425WHZ_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR340BXT


title: miR-7_purification2_4percent_rep4


title: ERF

description:
Raw file(s):
ENCFF781KGN_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR159DQO

value: FLAG-ERF


title: NFE2L2

description:
Re-analysis of:
GSM2423561 GSM2423560
Raw file(s):
ENCFF002EAS ENCFF002EAY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR488EES


title: miR-7_purification2_4percent_rep3


title: miR-7_purification2_4percent_rep2


title: miR-7_purification2_1.265percent_rep1


title: Col0_MS_root_for_hy5_rep3

type: RNA

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: root of 4-wk old plant grown(control for hy5-215)

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on MS-based agar media in growth chamber at 23 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

tag: genotype

value: wild type Col-0

tag: tissue

value: root

tag: light

value: normal white light

tag: nutrient condition

value: phosphate sufficient


title: Col0_P_deficiency_leaf_for_hy5_rep3

source_name: leaf of 4-wk old plant grown(control for hy5-215)

value: leaf

value: phosphate deficient


title: Col0_MS_root_for_hy5_rep2


title: Col0_P_deficiency_root_for_hy5_rep3


title: CBX5


title: Col0_P_deficiency_leaf_for_hy5_rep1


title: miR-7_purification2_4percent_rep1


title: Col0_P_deficiency_root_for_hy5_rep1


title: Col0_P_deficiency_root_for_hy5_rep2


title: miR-7_purification2_12.65percent_rep2


title: Col0_MS_root_for_hy5_rep1


title: Col0_MS_leaf_for_hy5_rep3


title: Col0_MS_leaf_for_hy5_rep1


title: Col0_MS_leaf_for_hy5_rep2


title: hy5_P_deficiency_root_rep3

source_name: root of 4-wk old plant grown


title: hy5_P_deficiency_root_rep2


title: Col0_P_deficiency_leaf_for_hy5_rep2


title: hy5_MS_root_rep3


title: hy5_P_deficiency_root_rep1


title: miR-7_purification2_12.65percent_rep1


title: hy5_MS_root_rep2


title: hy5_MS_root_rep1


title: hy5_P_deficiency_leaf_rep2

source_name: leaf of 4-wk old plant grown


title: CtC57ActDRGC3

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to mouse genome GRCm38 with the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

source_name: Mouse retina, 6-8 wk old

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90 and CD45 (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl. 30µM ActinomycinD (Millipore Sigma) was added to the oxygenated AMES, papain, and ovomucoid solutions. Cells were then resuspended in AMES + 4%BSA + 3µM ActinomycinD prior to FACS sorting.  Cells were FACS sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP co-expression. Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.

treatment_protocol: Vglut2:cre;Stp15 and C57BL/6J mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

value: retina

tag: age

value: 6-8 wk old


title: CtC57ActDRGC2


title: hy5_P_deficiency_leaf_rep3


title: KO4

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 “TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35”
MAPPING - STAR_2.6.0c “--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical”
READ COUNTING - subread-1.6.1 “featurecounts, -s 2 -t exon -g gene_name”
Genome_build: (GRCm38.p6) + Gencode-M17 Annotation
Supplementary_files_format_and_content: normalized abundance measurements

growth_protocol: Mouse lung endothelial cells were isolated and cultured as described in our recent publication in detail (Wang et al., Scientific Report, 2019 Feb 6;9(1):1458). Samples were collected from 2 different cohort of mice.

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary culture of endothelial cells without treatment were used for RNA-seq.

tag: cell type

value: Mouse lung endothelial cells (MLECs)

value: ZMPSTE24 knockout (ko)


title: ARID5B


title: miR-7_purification2_40percent_rep3


title: KO3

tag: genotype/variation


title: miR-7_purification2_40percent_rep4


title: miR-7_purification2_40percent_rep1


title: miR-7_purification2_40percent_rep2


title: ActR1GLAST


title: KO2


title: hy5_MS_leaf_rep2


title: miR-7_purification2_inputlibrary_rep2

value: inputlibrary


title: KO1


title: Col0_P_deficiency_root_for_BBX32SRDX_rep2

source_name: root of 4-wk old plant grown(control for 35S::BBX32-SRDX)


title: hy5_MS_leaf_rep3


title: miR-7_purification2_inputlibrary_rep1


title: hy5_MS_leaf_rep1


title: hy5_P_deficiency_leaf_rep1


title: Col0_P_deficiency_root_for_BBX32SRDX_rep3


title: WT2

value: ZMPSTE24 wild type (wt)


title: miR-7_purification1_inputlibrary2

description:
agorbns_miR-7_sitecounts.txt
agorbns_miR-7_nt1-4_12mer_kds.txt
agorbns_miR-7_nt2-5_12mer_kds.txt
agorbns_miR-7_nt3-6_12mer_kds.txt
agorbns_miR-7_nt4-7_12mer_kds.txt
agorbns_miR-7_nt5-8_12mer_kds.txt


title: Col0_P_deficiency_root_for_BBX32SRDX_rep1


title: miR-7_purification1_0percent


title: WT1


title: Col0_MS_root_for_BBX32SRDX_rep2


title: Col0_MS_root_for_BBX32SRDX_rep1


title: miR-7_purification1_0.4percent


title: miR-7_purification1_12.65percent


title: Col0_P_deficiency_leaf_for_BBX32SRDX_rep3

source_name: leaf of 4-wk old plant grown(control for 35S::BBX32-SRDX)


title: Col0_P_deficiency_leaf_for_BBX32SRDX_rep2


title: miR-7_purification1_1.265percent


title: miR-7_purification1_40percent


title: miR-7_purification1_inputlibrary


title: Col0_MS_leaf_for_BBX32SRDX_rep2


title: Col0_MS_root_for_BBX32SRDX_rep3


title: Col0_MS_leaf_for_BBX32SRDX_rep3


title: CrC571wCD90CD45CD140aR1

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples at each time point

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90, CD45 and CD140a (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP co-expression. Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)

value: retinal ganglion cells

tag: time point


title: let-7a,miR-155,miR-124,lsy-6_purification1_inputlibrary2


title: Col0_P_deficiency_leaf_for_BBX32SRDX_rep1


title: CrC571wCD90CD45CD140aR2


title: Col0_MS_leaf_for_BBX32SRDX_rep1


title: BBX32SRDX_P_deficiency_root_rep3


title: BBX32SRDX_P_deficiency_root_rep2


title: BBX32SRDX_P_deficiency_leaf_rep3


title: BBX32SRDX_MS_root_rep2


title: BBX32SRDX_MS_root_rep3


title: BBX32SRDX_P_deficiency_leaf_rep2


title: BBX32SRDX_MS_root_rep1


title: BBX32SRDX_P_deficiency_root_rep1


title: E2F7_iso1


title: CrVg1wCD90R2


title: lsy-6_purification1_1.265percent

description:
agorbns_lsy-6_sitecounts.txt
agorbns_lsy-6_nt1-4_12mer_kds.txt
agorbns_lsy-6_nt2-5_12mer_kds.txt
agorbns_lsy-6_nt3-6_12mer_kds.txt
agorbns_lsy-6_nt4-7_12mer_kds.txt
agorbns_lsy-6_nt5-8_12mer_kds.txt


title: CrVg4dCD45CD140aR1


title: CrVg1wCD90R1


title: BBX32SRDX_MS_leaf_rep2


title: CrVg4dCD90R1


title: col0_root_red_light_P_sufficient_rep1

source_name: root of 3-wk seedlings grown

value: red light


title: lsy-6_purification1_4percent


title: CrC574dCD90R2


title: BBX32SRDX_P_deficiency_leaf_rep1


title: lsy-6_purification1_0.4percent


title: CrC574dCD90R1


title: miR-124_purification2_0percent_rep2


title: lsy-6_purification1_12.65percent


title: col0_root_blue_light_P_sufficient_rep1

value: blue light


title: lsy-6_purification1_40percent

value: purified AGO2–miRNA complexes


title: col0_root_red_light_P_defficient_rep2


title: BBX32SRDX_MS_leaf_rep1


title: col0_root_red_light_P_sufficient_rep2


title: col0_root_red_light_P_defficient_rep1


title: BBX32SRDX_MS_leaf_rep3


title: CrVg2dCD45CD90R1


title: miR-124_purification2_0percent_rep1


title: col0_root_blue_light_P_defficient_rep2


title: CrC572dCD90R2


title: col0_shoot_red_light_P_defficient_rep2

source_name: shoot of 3-wk seedlings grown

value: shoot


title: col0_root_blue_light_P_defficient_rep1

value: wild type Col-0


title: CrC572dCD90R1


title: miR-124_purification2_0.4percent_rep2


title: col0_shoot_red_light_P_sufficient_rep2


title: col0_root_blue_light_P_sufficient_rep2

value: root


title: col0_shoot_red_light_P_sufficient_rep1


title: miR-124_purification2_0.4percent_rep1


title: col0_shoot_red_light_P_defficient_rep1


title: col0_shoot_blue_light_P_sufficient_rep1


title: CrC572dCD45CD90R1


title: col0_shoot_blue_light_P_defficient_rep1


title: CrC572dCD45CD140aR1


title: miR-124_purification2_4percent_rep2


title: CrVg1dCD45CD90R1


title: miR-124_purification2_1.265percent_rep1


title: Input 37

description:
Re-analysis of:
GSM935604
Raw file(s):
ENCFF000XTF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEN
Input for ARID3A
Input for BHLHE40
Input for BRCA1
Input for CEBPB
Input for CEBPZ
Input for CHD2
Input for IRF3
Input for JUND
Input for JUN
Input for MAFF
Input for MAFK
Input for MAZ
Input for POLR2A
Input for POLR2AphosphoS2
Input for RCOR1
Input for RFX5
Input for SMC3
Input for TBP


title: CrC571dCD90R1


title: miR-124_purification2_4percent_rep1


title: miR-124_purification2_1.265percent_rep2


title: CrC571dCD90R2


title: Input 36

description:
Re-analysis of:
GSM935444
Raw file(s):
ENCFF000XQR ENCFF000XQS
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EES
Input for ESRRA
Input for HSF1
Input for NR3C1


title: H. polygyrus bakeri-rechallenge Bhlhe40WT CD4 T cells rep3

city: St. Louis

first: Brian

middle: T

last: Edelson

state: MO

address: 425 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: hybridization performed by the Genome Technology Access Core (WUSTL)

data_processing: DNASTAR ArrayStar program using the RMA quantile method of normalization

label: biotin

source_name: proximal small intestine digest

extract_protocol: RNA isolated with E.Z.N.A. MicroElute Total RNA kit (Omega Bio-Tek)

tag: background strain

value: proximal small intestine

value: CD4 T cells

tag: treatment

value: H. polygyrus bakeri secondary infection

tag: gender

value: male


title: Input 34

description:
Re-analysis of:
GSM822314
Raw file(s):
ENCFF000RUP
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000DLT
Input for MYC

tag: cell line


title: Input 35

description:
Re-analysis of:
GSM935443
Raw file(s):
ENCFF000XRI ENCFF000XRH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EER
Input for SREBF1


title: CrC571dCD45CD140aR1

value: retina


title: H. polygyrus bakeri-rechallenge Bhlhe40KO CD4 T cells rep2

scan_protocol: performed by the Genome Technology Access Core (WUSTL)


title: miR-124_purification2_12.65percent_rep2

tag: miRNA

tag: rbp


title: miR-124_purification2_12.65percent_rep1

tag: ago–mirna complex purification

tag: sampletype


title: Input 32

description:
Re-analysis of:
GSM803521 GSM803463
Raw file(s):
ENCFF000POC ENCFF000POU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLN https://www.encodeproject.org/experiments/ENCSR000BLG
Input for ATF3
Input for FOXA1
Input for HNF4A

tag: chip antibody


title: H. polygyrus bakeri-rechallenge Bhlhe40WT CD4 T cells rep1

label_protocol: performed by the Genome Technology Access Core (WUSTL)

tag: genotype


title: H. polygyrus bakeri-rechallenge Bhlhe40KO CD4 T cells rep1

tag: tissue


title: H. polygyrus bakeri-rechallenge Bhlhe40KO CD4 T cells rep3


title: Input 31

description:
Re-analysis of:
GSM803521
Raw file(s):
ENCFF000POC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLN
Input for SIN3A


title: H. polygyrus bakeri-rechallenge Bhlhe40WT CD4 T cells rep2


title: miR-124_purification2_40percent_rep1

tag: rep


title: miR-124_purification2_40percent_rep2


title: Input 30

description:
Re-analysis of:
GSM803521
Raw file(s):
ENCFF000POC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLN
Input for FOSL2
Input for RXRA
Input for USF1


title: Naïve Bhlhe40KO CD4 T cells rep1

value: untreated


title: Naïve Bhlhe40KO CD4 T cells rep2


title: Naïve Bhlhe40WT CD4 T cells rep1


title: col0_shoot_blue_light_P_defficient_rep2

tag: light

tag: nutrient condition

value: phosphate deficient


title: Naïve Bhlhe40WT CD4 T cells rep2

tag: cell type


title: CrC571dCD45CD90R1

tag: age

value: 6-8 wk old


title: Input 29

description:
Re-analysis of:
GSM803463
Raw file(s):
ENCFF000POV ENCFF000POU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLG
Input for CEBPD
Input for CTCF
Input for EP300
Input for HDAC2
Input for HNF4G
Input for POLR2AphosphoS5
Input for REST
Input for SRF
Input for YY1
Input for ZBTB33
Input for ZBTB7A


title: Input 28

description:
Re-analysis of:
GSM803462
Raw file(s):
ENCFF000POQ ENCFF000POO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLH
Input for TAF1


title: Input 3

description:
Re-analysis of:
GSM1010814
Raw file(s):
ENCFF000PPC ENCFF000PPF ENCFF000PPI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BPH
Input for MAX
Input for MBD4
Input for MYBL2
Input for NFIC
Input for NR2F2
Input for SP2
Input for TEAD4
Input for ZEB1


title: ZNF274

description:
Re-analysis of:
GSM935350
Raw file(s):
ENCFF000XZX ENCFF000XZW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EVR


title: miR-124_purification2_inputlibrary_rep2

value: inputlibrary


title: CrC5712hCD90R1

tag: time point


title: CrC5712hCD45CD90CD140aR1


title: Input 2

description:
Re-analysis of:
GSM1010814
Raw file(s):
ENCFF270NSD ENCFF000PPF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BPH https://www.encodeproject.org/experiments/ENCSR399MAN
Input for FOXA2


title: ZBTB7A

description:
Re-analysis of:
GSM1010831
Raw file(s):
ENCFF000PTI ENCFF000PTF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BQA


title: CtVgCD90R1

value: control


title: miR-124,lsy-6_purification1_0percent

description:
agorbns_miR-124_sitecounts.txt
agorbns_miR-124_nt1-4_12mer_kds.txt
agorbns_miR-124_nt2-5_12mer_kds.txt
agorbns_miR-124_nt3-6_12mer_kds.txt
agorbns_miR-124_nt4-7_12mer_kds.txt
agorbns_miR-124_nt5-8_12mer_kds.txt
agorbns_lsy-6_sitecounts.txt
agorbns_lsy-6_nt1-4_12mer_kds.txt
agorbns_lsy-6_nt2-5_12mer_kds.txt
agorbns_lsy-6_nt3-6_12mer_kds.txt
agorbns_lsy-6_nt4-7_12mer_kds.txt
agorbns_lsy-6_nt5-8_12mer_kds.txt


title: ZEB1

description:
Re-analysis of:
GSM1010809
Raw file(s):
ENCFF000PTQ ENCFF000PTO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BVN


title: CrC5712hCD90R3

value: retinal ganglion cells


title: YY1

description:
Re-analysis of:
GSM803381
Raw file(s):
ENCFF000PSD ENCFF000PSE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BNT


title: ZBTB33

description:
Re-analysis of:
GSM803418
Raw file(s):
ENCFF000PST ENCFF000PSY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BNA


title: USF1

description:
Re-analysis of:
GSM803527
Raw file(s):
ENCFF000PSH ENCFF000PSA
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BGM


title: col0_shoot_blue_light_P_sufficient_rep2

value: phosphate sufficient


title: miR-124_purification1_0.4percent

description:
agorbns_miR-124_sitecounts.txt
agorbns_miR-124_nt1-4_12mer_kds.txt
agorbns_miR-124_nt2-5_12mer_kds.txt
agorbns_miR-124_nt3-6_12mer_kds.txt
agorbns_miR-124_nt4-7_12mer_kds.txt
agorbns_miR-124_nt5-8_12mer_kds.txt


title: miR-124_purification1_1.265percent


title: TBP

description:
Re-analysis of:
GSM935280
Raw file(s):
ENCFF000XZI ENCFF000XZL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEL

value: TBP


title: CtC57CD90R1


title: CtC57CD45CD90R1


title: miR-124_purification1_4percent

value: purified AGO2–miRNA complexes


title: TAF1

description:
Re-analysis of:
GSM803367
Raw file(s):
ENCFF000PRB ENCFF000PRD
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BJN


title: miR-124_purification2_inputlibrary_rep1


title: miR-124_purification1_12.65percent


title: SRF

description:
Re-analysis of:
GSM803502
Raw file(s):
ENCFF000PQU ENCFF000PQW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLV

value: SRF


title: SREBF1

description:
Re-analysis of:
GSM935627
Raw file(s):
ENCFF000XYE ENCFF000XYB
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEO


title: CtC57CD45CD90P2


title: SP2

description:
Re-analysis of:
GSM1010787
Raw file(s):
ENCFF000PQL ENCFF000PQP
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BOU


title: RFX5

description:
Re-analysis of:
GSM935304
Raw file(s):
ENCFF000XXZ ENCFF000XXX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEA


title: SMC3

description:
Re-analysis of:
GSM935542
Raw file(s):
ENCFF000XXY ENCFF000XYC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDW


title: miR-124,lsy-6_purification1_inputlibrary


title: CtVgCD45CD90R1


title: miR-155_purification1_0percent

description:
agorbns_miR-155_sitecounts.txt
agorbns_miR-155_nt1-4_12mer_kds.txt
agorbns_miR-155_nt2-5_12mer_kds.txt
agorbns_miR-155_nt3-6_12mer_kds.txt
agorbns_miR-155_nt4-7_12mer_kds.txt
agorbns_miR-155_nt5-8_12mer_kds.txt


title: SIN3A

description:
Re-analysis of:
GSM803530
Raw file(s):
ENCFF000PPW ENCFF000PQC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BGL


title: CtC57CD45CD90P1


title: REST

description:
Re-analysis of:
GSM1010784
Raw file(s):
ENCFF000PMU ENCFF000PMV
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BOT

value: REST


title: miR-155_purification1_0.4percent


title: TEAD4

description:
Re-analysis of:
GSM1010875
Raw file(s):
ENCFF000PRQ ENCFF000PRU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BRP


title: POLR2AphosphoS5

description:
Re-analysis of:
GSM1010821
Raw file(s):
ENCFF000PNL ENCFF000PNI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BPI


title: RCOR1

description:
Re-analysis of:
GSM935579
Raw file(s):
ENCFF000XQW ENCFF000XQY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDQ


title: miR-155_purification1_1.265percent


title: NR3C1

description:
Re-analysis of:
GSM935620
Raw file(s):
ENCFF000XRU ENCFF000XRV
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEV


title: miR-155_purification1_4percent


title: NR2F2

description:
Re-analysis of:
GSM1010810
Raw file(s):
ENCFF000PMC ENCFF000PMF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BVM


title: MYC

description:
Re-analysis of:
GSM822291
Raw file(s):
ENCFF000RTY ENCFF000RTX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000DLR

value: MYC


title: NR2C2

description:
Re-analysis of:
GSM935596
Raw file(s):
ENCFF000XZK ENCFF000XZJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EVS


title: NFIC

description:
Re-analysis of:
GSM1010741
Raw file(s):
ENCFF000PMB ENCFF000PLW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BQX

value: NFIC


title: miR-155_purification1_12.65percent


title: MYBL2

description:
Re-analysis of:
GSM1010876
Raw file(s):
ENCFF000PLP ENCFF000PLM
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BRO


title: miR-155_purification1_40percent


title: RXRA

description:
Re-analysis of:
GSM803452
Raw file(s):
ENCFF000PPM ENCFF000PPQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BHU

value: RXRA


title: let-7a_purification1_0percent

description:
agorbns_let-7a_sitecounts.txt
agorbns_let-7a_nt1-4_12mer_kds.txt
agorbns_let-7a_nt2-5_12mer_kds.txt
agorbns_let-7a_nt3-6_12mer_kds.txt
agorbns_let-7a_nt4-7_12mer_kds.txt
agorbns_let-7a_nt5-8_12mer_kds.txt


title: MBD4

description:
Re-analysis of:
GSM1010740
Raw file(s):
ENCFF000PLH ENCFF000PLF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BQW


title: CrC5712hCD90R2


title: let-7a_purification1_0.4percent


title: MAZ

description:
Re-analysis of:
GSM935335
Raw file(s):
ENCFF000XUP ENCFF000XUN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDN

value: MAZ


title: MAX

description:
Re-analysis of:
GSM1010865
Raw file(s):
ENCFF000PKZ ENCFF000PKX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BTM

value: MAX


title: MAFK

description:
Re-analysis of:
GSM935305
Raw file(s):
ENCFF000XUK ENCFF000XUL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEB

value: MAFK


title: let-7a_purification1_1.265percent


title: MAFF

description:
Re-analysis of:
GSM935306
Raw file(s):
ENCFF000XUA ENCFF000XTZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEC

value: MAFF


title: JUND

description:
Re-analysis of:
GSM935649
Raw file(s):
ENCFF000XTR ENCFF000XTQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEI

value: JUND


title: let-7a_purification1_4percent


title: JUN

description:
Re-analysis of:
GSM935364
Raw file(s):
ENCFF000XQT ENCFF000XQU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEK

value: JUN


title: IRF3

description:
Re-analysis of:
GSM935650
Raw file(s):
ENCFF000XTO ENCFF000XTN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEJ


title: POLR2AphosphoS2

description:
Re-analysis of:
GSM935543
Raw file(s):
ENCFF000XXC ENCFF000XXB
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDX


title: POLR2A

description:
Re-analysis of:
GSM935603
Raw file(s):
ENCFF000XWJ ENCFF000XWR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEM


title: let-7a_purification1_12.65percent


title: Input 27

description:
Re-analysis of:
GSM733732
Raw file(s):
ENCFF000BDT ENCFF000BDZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000AME
Input for ASH2L
Input for BMI1
Input for BRD4
Input for EZH2
Input for KDM1A
Input for KDM6A
Input for RING1


title: Input 33

description:
Re-analysis of:
GSM817343
Raw file(s):
ENCFF000XTE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EVT
Input for MXI1
Input for NR2C2
Input for TCF7L2
Input for ZNF274


title: HSF1

description:
Re-analysis of:
GSM935626
Raw file(s):
ENCFF000XSL ENCFF000XSK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EET


title: HNF4G

description:
Re-analysis of:
GSM803404
Raw file(s):
ENCFF000PKJ ENCFF000PKH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BNJ


title: HNF4A

description:
Re-analysis of:
GSM803460
Raw file(s):
ENCFF000PJX ENCFF000PJT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLF


title: MXI1

description:
Re-analysis of:
GSM935437
Raw file(s):
ENCFF000XUX ENCFF000XVA
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDU


title: HDAC2

description:
Re-analysis of:
GSM803493
Raw file(s):
ENCFF000PJJ ENCFF000PJD
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BMC


title: let-7a_purification1_40percent

description:
agorbns_let-7a_sitecounts.txt
agorbns_let-7a_nt1-4_12mer_kds.txt
agorbns_let-7a_nt2-5_12mer_kds.txt
agorbns_let-7a_nt3-6_12mer_kds.txt
agorbns_let-7a_nt4-7_12mer_kds.txt
agorbns_let-7a_nt5-8_12mer_kds.txt


title: FOXA1

description:
Re-analysis of:
GSM803461
Raw file(s):
ENCFF000PIM ENCFF000PIJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLE


title: let-7a,miR-155_purification1_inputlibrary

description:
agorbns_let-7a_sitecounts.txt
agorbns_let-7a_nt1-4_12mer_kds.txt
agorbns_let-7a_nt2-5_12mer_kds.txt
agorbns_let-7a_nt3-6_12mer_kds.txt
agorbns_let-7a_nt4-7_12mer_kds.txt
agorbns_let-7a_nt5-8_12mer_kds.txt
agorbns_miR-155_sitecounts.txt
agorbns_miR-155_nt1-4_12mer_kds.txt
agorbns_miR-155_nt2-5_12mer_kds.txt
agorbns_miR-155_nt3-6_12mer_kds.txt
agorbns_miR-155_nt4-7_12mer_kds.txt
agorbns_miR-155_nt5-8_12mer_kds.txt

value: inputlibrary


title: FOS

description:
Raw file(s):
ENCFF002EDT_in_progress ENCFF002EDV_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR177HDZ

value: FOS


title: FOSL2

description:
Re-analysis of:
GSM803451
Raw file(s):
ENCFF000PIE ENCFF000PHU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BHP


title: miR-1_purification3_0percent


title: ESRRA

description:
Re-analysis of:
GSM935621
Raw file(s):
ENCFF000XRO ENCFF000XRN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEW

value: ESRRA


title: EP300

description:
Re-analysis of:
GSM803499
Raw file(s):
ENCFF000PMZ ENCFF000PNA
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BLW


title: miR-124_purification1_40percent

description:
agorbns_miR-124_sitecounts.txt
agorbns_miR-124_nt1-4_12mer_kds.txt
agorbns_miR-124_nt2-5_12mer_kds.txt
agorbns_miR-124_nt3-6_12mer_kds.txt
agorbns_miR-124_nt4-7_12mer_kds.txt
agorbns_miR-124_nt5-8_12mer_kds.txt


title: CHD2

description:
Re-analysis of:
GSM935307
Raw file(s):
ENCFF000XQP ENCFF000XQQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EED


title: CUX1

description:
Raw file(s):
ENCFF002EDX_in_progress ENCFF002EDU_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR049KIZ


title: smallRNA-seq_purifiedAGO2-miR-1

description:
Small RNAs associated with purified AGO2
smallRNA-seq_counts.txt
smallRNA-seq_cpm.txt

data_processing:
Each read was used if it satisfied the following criteria: 1) it passed the Illumina chastity filter, as indicated by the presence of the number 1 rather than 0 in the final position of the fastq header line, 2) it did not contain any “N” base calls, 3) it did not contain any positions with a Phred quality score (Q) of B or lower, 4) the sequenced 6-nt sample-multiplexing barcode associated with the read was identical to one of the barcodes used when generating the sequencing library, and 5) it did not match either strand of the phi-X genome.
To count the miRNAs in each library, the sequence corresponding to the first 18 nucleotides following the 5′ adapter of each read was queried against a list of the first 18 nucleotides of human miRNAs annotated in miRbase_v21, supplemented with the 5′ and 3′ adapter sequences, the 18- and 30-nt marker sequences, and the dme-miR-14-5p and xtr-miR-427 sequences.
Counts were normalized to the total number of counts corresponding to human miRNAs to obtain counts-per-million (cpm) values.
Genome_build: NA
Supplementary_files_format_and_content: Two tab delimited text files containing either 1) the total sequencing counts for all human miRNAs in miRbase_v21 supplemented with the 5′ and 3′ adapter sequences, the 18- and 30-nt marker sequences, and the dme-miR-14-5p and xtr-miR-427 sequences in each of the two purified AGO2 preparations, or 2) the counts-per-million (cpm) corresponding to each.

source_name: purified AGO2?miRNA complexes

growth_protocol: Each HEK293T sample was grown or maintained according to standard protocols.

extract_protocol:
RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing according to the methods.

treatment_protocol: AGO2 overexpression, loading, and purification was performed according to the methods.

tag: overexpression


title: miR-1_purification3_4percent


title: CEBPZ

description:
Re-analysis of:
GSM935274
Raw file(s):
ENCFF000XPZ ENCFF000XQB
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDO

value: CEBPZ


title: miR-1_purification3_0.4percent


title: CTCF

description:
Re-analysis of:
GSM803486
Raw file(s):
ENCFF000PHG ENCFF000PHE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BIE

value: CTCF


title: BRCA1

description:
Re-analysis of:
GSM935609
Raw file(s):
ENCFF000XPL ENCFF000XPS
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDY


title: CEBPD

description:
Re-analysis of:
GSM1010777
Raw file(s):
ENCFF000PGK ENCFF000PGQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BQJ

value: CEBPD


title: BACH1

description:
Raw file(s):
ENCFF002EDR_in_progress ENCFF002EDO_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR699TNT


title: miR-1_purification3_inputlibrary

value: purified AGO2–miRNA complexes


title: smallRNA-seq_purifiedAGO2-miR-155


title: ATF3

description:
Re-analysis of:
GSM803503
Raw file(s):
ENCFF000PFQ ENCFF000PFR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000BKE


title: miR-1_purification3_12.65percent


title: miR-1_purification3_40percent


title: CEBPB

description:
Re-analysis of:
GSM935493
Raw file(s):
ENCFF000XQM ENCFF000XQN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EEE

value: CEBPB


title: ARID3A

description:
Re-analysis of:
GSM935275
Raw file(s):
ENCFF000XOS ENCFF000XOU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDP


title: Exp85

source_name: PBMC primary cells from donor

value: PBMC primary cells from donor

tag: molecule type

value: various proteins


title: miR-1_purification2_0.4percent

description:
agorbns_miR-1_sitecounts.txt
agorbns_miR-1_nt1-4_12mer_kds.txt
agorbns_miR-1_nt2-5_12mer_kds.txt
agorbns_miR-1_nt3-6_12mer_kds.txt
agorbns_miR-1_nt4-7_12mer_kds.txt
agorbns_miR-1_nt5-8_12mer_kds.txt


title: Exp72


title: miR-1_purification2_0percent


title: miR-1_purification2_4percent


title: miR-1_purification2_1.265percent


title: BHLHE40

description:
Re-analysis of:
GSM935566
Raw file(s):
ENCFF000XPC ENCFF000XPA
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDT


title: miR-1_purification2_12.65percent


title: miR-1_purification2_inputlibrary


title: miR-1_purification2_40percent


title: WT4_xl_BamHI-HF_200U_30min

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Library strategy: ORE-seq
ORE-seq: cut and uncut fragment count and resection length  After demultiplexing (Girardot et al. 2016), sequenced reads were trimmed based on basecalling quality and mapped (Li and Durbin 2009) using the combined S. cerevisiae and S. pombe reference genome. Fragments longer than 500 bp or on rDNA loci were removed. At each cut site, fragment starts and ends were counted within a sample-specific window (green areas in Fig. S1D, see Supplemental Methods) to account for exonuclease resection and within the same window the mean resection length was calculated. Uncut fragments, i.e. fragments covering, but not starting or ending at the cut site, were also counted at each cut site. Cut sites with neighbours closer than 200 bp were ignored completely and remaining cut sites with neighbours closer than 300 bp were analysed only using the starting/ending counts not pointing towards the close neighbour.  ORE-seq: occupancy estimation (cut-uncut method) See Methods and Supplemental Methods.
Calculation of ORE-seq and ODM-seq maps  For RE samples, very rare occupancy estimates outside of the interval between 0 and 1 were truncated to 0 or 1. For the ORE-seq map (Fig. 1B) we averaged the occupancy values at the same sites in different RE samples with equal weights. Similarly, for the ODM-seq map (Fig. 1B), different bisulfite samples were averaged with equal weights. We also calculated individual enzyme maps in the same way (attached as supplementary file).
BedGraph files contain the (corrected) absolute occupancy values and were generated using the R (R_Core_Team 2018) package rtracklayer (Lawrence et al. 2013).
tsv files contain columns with the absolute occupancy (corrected and not corrected), the number of effective cuts and the effective coverage for each RE site.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph, tsv

organism: Saccharomyces cerevisiae

source_name: chromatin

growth_protocol: The BY4741 strain (MATa his3D0 leu2D0 met15D0 ura3D0, Euroscarf) was grown to log phase (Supplemental Fig. S1A) in YPDA medium (1% w/v Bacto yeast extract, 2% w/v Bacto peptone, 2% w/v glucose, 0.1 g/l adenine, 1 g/l KH2PO4).

extract_protocol:
Nuclei from ca. 0.1 g wet cell pellet were pre-washed in methylation buffer, centrifuged and resuspended either in 400 µl 1x CutSmart buffer (NEB) for BamHI-HF and AluI or in 1x NEB2.1 for HindIII. Digestions were started by RE addition, incubated for 30 or 120 minutes at 37°C and stopped by 10 mM EDTA and 0.5% SDS (final conc.). DNA preparation was as above. For the cut-all cut method, Schizosaccharomyces pombe gDNA, fully digested with the corresponding RE, was spiked in at 5-10% DNA mass of the final sample before phenol-chloroform extraction. After RNase A digestion, half of the sample was digested for a second time with 100 U of the corresponding RE and in the corresponding buffer for 1.5 h at 37°C. The reaction was stopped by 15 mM EDTA (final conc.).
Purified DNA was sheared to ~150 bp fragments with the Covaris S220 and concentrated using the NucleoSpin Gel and PCR Clean-up Kit (Macherey&Nagel). 0.5 – 1 µg as determined by Qubit (ThermoFisher Scientific) was used for library preparation. First, DNA was end polished (15 U T4 DNA Polymerase, 50 U T4 PNK, 5 U Klenow (NEB)) for 30 minutes at 20°C, purified with AmPure XP beads (Beckman Coulter), then subjected to A-tailing (15 U Klenow exo-(NEB)) for 30 minutes at 37°C and purified again. For adapter ligation 15 U T4 DNA Ligase (NEB) and 75 to 150 pmol NEBNext Adaptor or NEBNext Methylated Adaptor for bisulfite conversion were added. The reaction was incubated for 20 minutes at 25°C followed again by AmPure XP bead purification. Half of the end-polished and adapter ligated sample was subjected to 8 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion Polymerase (NEB). Methylated samples were bisulfite converted following the manufacturer’s instructions of the Qiagen EpiTect Bisulfite Kit. 3 µl of the converted sample was subjected to 12-14 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion U Polymerase (ThermoFisher Scientific). All samples were sequenced by LaFuGa (Illumina HiSeq 1500, 50 bp paired-end mode).

treatment_protocol: Yeast nuclei were prepared as described (Almer et al. 1986). In brief, cells were harvested by centrifugation, washed in water, resuspended in 2.8 mM EDTA, pH 8, 0.7 M 2-mercaptoethanol, incubated for 30 minutes at 30°C, washed in 1 M sorbitol, resuspended in 1 M sorbitol, 5 mM 2-mercaptoethanol and spheroplasted by incubation with 20 mg/ml freshly added Zymolyase 100T (MP Biochemicals) for 30 minutes at 30°C. Spheroplasts were washed with 1 M sorbitol and resuspended in lysis buffer (18% Ficoll, 20 mM KH2PO4, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA) followed by centrifugation at 22,550 g for 30 min to collect chromatin (“nuclei”). Pellets were frozen in dry-ice/ethanol and stored at -80°C.

tag: restriction enzyme (re)

value: BamHI-HF

tag: strain

value: BY4741 - Replicate 4

tag: units of re/incubation time


title: WT4_xl_BamHI-HF_800U_30min_rep1


title: WT4_xl_BamHI-HF_800U_120min_200U_at_1h

value: 800 + refill/ 120 min


title: WT4_xl_HindIII_1000U_30min

value: HindIII


title: WT4_xl_BamHI-HF_800U_30min_rep2


title: miR-1_purification1_10percent

tag: miRNA

tag: rbp


title: WT4_xl_HindIII_0U_30min


title: mirna_11

first: Bin

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing data were aligned to the reference human genome (UCSC hg19) and EBV genome (GCF_000872045.1).
Reads mapped to known miRNAs were identified by searching miRBase database (v21). Novel miRNAs were predicted by miRDeep. Known and novel miRNA expression levels were measured by the number of mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw read count

source_name: nasopharyngeal mucosal specimen

extract_protocol:
Total RNA was extracted from NPC specimens and normal nasopharyngeal mucosal specimens using TRIzol reagent (Invitrogen; Carlsbad, CA, USA). The RNA concentration was measured with a NanoDrop2000 Spectrophotometer (NanoDrop Technologies; Wilmington, DE, USA), and the integrity of purified RNA was determined using Agilent 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA USA). miRNA quantification was evaluated using Hot Start PCR.
A small RNA library was built using the Next Multiplex Small RNA Library Prep Set for Illumina (NEB; Ipswich, MA, USA) according to the manufacturer’s protocol. Polyacrylamide gel electrophoresis was performed to purify small RNA and to enrich for molecules ranging from 18 to 30 nt. Then, cDNA was synthesized, digested and amplified to set cDNA libraries, followed by purification on a polyacrylamide gel and quantification.

value: nasopharyngeal mucosa

tag: disease status

value: Control


title: WT4_xl_AluI_400U_30min

value: AluI


title: Exp71

data_processing:
Library strategy: Single cell barcoding by split-pool synthesis via ligation
FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers


title: WT4_xl_BamHI-HF_0U_30min


title: WT4_xl_AluI_100U_30min


title: WT4_HindIII_1000U_30min


title: WT4_HindIII_4000U_30min


title: WT4_HindIII_0U_30min


title: WT4_BamHI-HF_800U_30min


title: WT4_xl_AluI_0U_30min


title: miR-1_purification3_1.265percent

tag: ago–mirna complex purification

tag: sampletype


title: WT4_xl_HindIII_4000U_30min


title: exp1_Exp92


title: WT4_AluI_400U_30min


title: WT4_BamHI-HF_200U_30min


title: mirna_10

tag: tissue


title: mirna_9


title: WT4_AluI_100U_30min


title: mirna_8


title: miR-1_purification1_inputlibrary

value: inputlibrary

tag: rep


title: WT3_HindIII_400U_30min

value: BY4741 - Replicate 3


title: WT3_HindIII_4000U_30min


title: WT3_HindIII_0U_30min


title: mirna_7

source_name: Nasopharyngeal carcinoma biopsy

value: nasopharyngeal carcinoma

value: NPC


title: WT3_BamHI-HF_200U_30min


title: WT3_BamHI-HF_800U_120min_200U_at_1h


title: WT3_BamHI-HF_800U_30min_rep1


title: mirna_3


title: mirna_2


title: mirna_4


title: mirna_1


title: WT3_BamHI-HF_0U_30min


title: WT2_BamHI-HF_100U_30min_rep2

value: BY4741 - Replicate 2


title: WT2_BamHI-HF_400U_30min_rep1


title: WT3_AluI_100U_30min


title: WT2_BamHI-HF_400U_30min_rep2


title: WT2_BamHI-HF_100U_30min_rep1


title: WT3_AluI_0U_30min


title: WT2_BamHI-HF_0U_30min_rep2


title: WT2_BamHI-HF_0U_30min_rep1


title: WT2_AluI_300U_30min


title: mrna_10

data_processing:
Paired-end RNA-seq data was generated with the Illumina HiSeq 4000 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg19 genome using star aligner (version 2.4.0g1).
Following read alignment, featureCounts (v1.4.6) was used to quantify the gene expression at the gene level based on Ensembl gene model version  70.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts

extract_protocol:
Total RNA was extracted from NPC specimens and normal nasopharyngeal mucosal specimens using TRIzol reagent (Invitrogen; Carlsbad, CA, USA). The RNA concentration was measured with a NanoDrop2000 Spectrophotometer (NanoDrop Technologies; Wilmington, DE, USA), and the integrity of purified RNA was determined using Agilent 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA USA). Then RNA was treated with Ribo-ZeroTM Magnetic Kit(Human) (Epicentre) to deplete rRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT2_AluI_100U_30min


title: WT3_BamHI-HF_800U_30min_rep2


title: mirna_6


title: mirna_5


title: WT1_xl_HindIII_4000U_30min

value: BY4741 - Replicate 1


title: mrna_9


title: mrna_8


title: WT1_xl_HindIII_0U_30min


title: WT3_AluI_400U_30min


title: mrna_7


title: mrna_6


title: WT1_xl_BamHI-HF_800U_30min_rep2


title: mrna_11


title: WT1_xl_BamHI-HF_800U_120min_200U_at_1h


title: WT1_xl_BamHI-HF_0U_30min


title: WT1_xl_AluI_400U_30min


title: mrna_5


title: Input 38

description: Input for CBX1

source_name: HepG2 cells

tag: cell line

tag: chip antibody


title: mrna_4


title: WT1_BamHI-HF_800U_120min_200U_at_1h


title: Input 39

description: Input for KLF10


title: Input 26

description:
Re-analysis of:
GSM2534659 GSM2533973
Raw file(s):
ENCFF434XRU ENCFF074CLV
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR945JOR https://www.encodeproject.org/experiments/ENCSR381PHD
Input for ZMYM3


title: WT1_xl_AluI_0U_30min


title: WT1_BamHI-HF_800U_30min


title: WT2_AluI_0U_30min


title: WT1_xl_AluI_100U_30min


title: WT1_BamHI-HF_100U_30min


title: WT1_BamHI-HF_400U_30min


title: WT1_xl_HindIII_1000U_30min


title: mrna_2


title: WT1_BamHI-HF_0U_30min


title: Input 25

description:
Re-analysis of:
GSM2534584
Raw file(s):
ENCFF255HDL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR882VRP
Input for ATF1


title: in_vitro_chromatin_low_dens_BamHI-HF_80U_30min

molecule: other

source_name: in vitro reconstituted chromatin

value: salt gradient dialysis chromatin low density


title: WT1_xl_BamHI-HF_800U_30min_rep1


title: mrna_1


title: in_vitro_chromatin_low_dens_BamHI-HF_80U_120min_20U_at_1h

value: 80 + refill/ 120 min


title: WT1_xl_BamHI-HF_200U_30min


title: Input 24

description:
Re-analysis of:
GSM2534538 GSM2534344
Raw file(s):
ENCFF002BFX ENCFF002BGD
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR855LCA https://www.encodeproject.org/experiments/ENCSR711HPO
Input for ZHX2


title: in_vitro_chromatin_low_dens_BamHI-HF_20U_30min


title: mrna_3


title: in_vitro_chromatin_high_dens_BamHI-HF_80U_120min_20U_at_1h

value: salt gradient dialysis chromatin high density


title: in_vitro_chromatin_high_dens_BamHI-HF_80U_30min


title: Input 22

description:
Re-analysis of:
GSM2534255 GSM2534356
Raw file(s):
ENCFF002BFY ENCFF876NBT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR716SYG https://www.encodeproject.org/experiments/ENCSR649FPL
Input for TFAP4


title: Input 20

description:
Re-analysis of:
GSM2534255
Raw file(s):
ENCFF002BFY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR649FPL
Input for RUVBL1


title: Input 23

description:
Re-analysis of:
GSM2534538 GSM2533973
Raw file(s):
ENCFF002BGD ENCFF434XRU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR855LCA https://www.encodeproject.org/experiments/ENCSR381PHD
Input for PROX1


title: in_vitro_chromatin_high_dens_BamHI-HF_20U_30min


title: Input 21

description:
Re-analysis of:
GSM2534255 GSM2534344
Raw file(s):
ENCFF002BFY ENCFF002BFX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR711HPO https://www.encodeproject.org/experiments/ENCSR649FPL
Input for NR1H2


title: calibration_HindIII_30_pct_cut_30min

source_name: genomic DNA

value: calibration sample 30%


title: calibration_HindIII_50_pct_cut_30min

value: calibration sample 50%


title: calibration_HindIII_90_pct_cut_30min

value: calibration sample 90%